Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.16.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80988	0.486
27DAP/17DAP	0.86471	0.677
39DAP/27DAP	1.86193	0.121
41DAP/39DAP	1.11841	0.742
42DAP/41DAP	0.48819	0.262
43DAP/42DAP	0.8267	0.698
47DAP/43DAP	0.80324	0.407
52DAP/47DAP	2.0396	0.242
57DAP/52DAP	0.86433	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10572	0.5
17DAP/reference	0.93225	0.224
27DAP/reference	0.95233	0.471
39DAP/reference	0.90134	0.09
41DAP/reference	0.9596	0.341
42DAP/reference	0.90338	0.045
43DAP/reference	0.96447	0.429
47DAP/reference	0.85252	0.032
52DAP/reference	0.92244	0.31
57DAP/reference	0.95615	0.199

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.41117	0.037
27DAP/17DAP	1.20885	0.645
39DAP/27DAP	0.91748	0.594
41DAP/39DAP	2.88545	0.042
42DAP/41DAP	0.45729	0.007
43DAP/42DAP	1.02352	1
47DAP/43DAP	1.16204	0.873
52DAP/47DAP	3.05609	0.044
57DAP/52DAP	2.80437	0.05
57DAP/7DAP	1.23177	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6535	0.042
17DAP/reference	1.02002	0.693
27DAP/reference	0.86651	0.058
39DAP/reference	1.50286	0.016
41DAP/reference	1.13057	0.35
42DAP/reference	1.37066	0.046
43DAP/reference	1.65089	0.007
47DAP/reference	1.44443	0.033
52DAP/reference	1.74834	0.007
57DAP/reference	1.58565	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07595	0.495
17DAP/reference	0.94011	0.297
27DAP/reference	0.90164	0.203
39DAP/reference	1.11953	0.059
41DAP/reference	1.06272	0.525
42DAP/reference	0.96191	0.237
43DAP/reference	0.96819	0.527
47DAP/reference	0.92675	0.097
52DAP/reference	1.027	0.789
57DAP/reference	1.0078	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35457	0.026
17DAP/reference	0.89809	0.144
27DAP/reference	0.99354	0.727
39DAP/reference	0.92008	0.271
41DAP/reference	0.87804	0.107
42DAP/reference	0.77902	0.071
43DAP/reference	0.79945	0.066
47DAP/reference	0.90675	0.191
52DAP/reference	1.04942	0.77
57DAP/reference	0.93396	0.127

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1715	0.966
26DAP/20DAP	1.21902
34DAP/26DAP	1.23247	1
51DAP/34DAP	1.08514	1
52DAP/51DAP	1.53679	0.092
53DAP/52DAP	0.97535	0.848
55DAP/53DAP	1.12341	1
57DAP/55DAP	0.89242	0.694
62DAP/57DAP	1.02068	1
68DAP/62DAP	1.00559	0.939
68DAP/14DAP	0.98281	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.27304	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.4587	0.021
Immature Eggplant/Mature Eggplant	1.17315
Ripe Pepper/Ripe Tomato	0.33517	0.224
Mature Eggplant/Ripe Tomato	1.27879	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.83294
12-2/M82	1.4663
12-4/M82	1.12733
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.43882	0.505
3-2/M82	0.98366	1
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.75321
5-3/M82	0.88123
6-2/M82	4.59196
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.09905	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82117	0.243
IL2-6/WTpooled	0.97812	1
IL7-5/WTpooled	0.59584	1
IL7-3/WTpooled	0.96009	1
IL12-4/WTpooled	1.01812	0.891
IL1-4/WTpooled	1.04352	1
WT/WTpooled	1.09119	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	2.17097	0.853

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07672	1
DC3000/delta hrp 6h	0.85941	0.95
DC3000/delta hrp 12h	0.83453	1
DC3000/delta hrp 24h	1.90347	0.051

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.82423

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85441	1
Exp 36h	1.87548	0.409
Exp 60h	1.5942	0.283

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.03719	1
Var 0h	0.79427	0.933
Var 12h I row2-row1	1.05283	0.692
Var 12h NI row2-row1	2.47327	0.649
Var 36h I row2-row1	1.3215	0.601
Var 36h NI row2-row1	1.12671
Var 60h I row2-row1	1.47749	0.487
Var 60h NI row2-row1	0.79011	0.63
Time course 0hI-0hNI	1.39414	0.537
Time course 12hI-12hNI	2.51181	0.004
Time course 36hI-36hNI	6.97463	0.004
Time course 60hI-60hNI	7.39158	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.51288	0.221
transgenic ySAMdc/azygous control (breaker)	0.22815	0.122
transgenic ySAMdc/azygous control (red)	1.47316	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02008	0.301

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95951	0.431

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80597	1
Manapal/WT (break)	0.60683	1
Manapal/WT (red)	0.3529	0.183